Cellular strategies for regulating DNA supercoiling: a single-molecule perspective.

Entangling and twisting of cellular DNA (i.e., supercoiling) are problems inherent to the helical structure of double-stranded DNA. Supercoiling affects transcription, DNA replication, and chromosomal segregation. Consequently the cell must fine-tune supercoiling to optimize these key processes. Here, we summarize how supercoiling is generated and review experimental and theoretical insights into supercoil relaxation. We distinguish between the passive dissipation of supercoils by diffusion and the active removal of supercoils by topoisomerase enzymes. We also review single-molecule studies that elucidate the timescales and mechanisms of supercoil removal.

Controlling the Quality Factor of a Single Acoustic Nanoresonator by Tuning its Morphology.

The mechanical vibrations of individual gold nanodisks nanopatterned on a sapphire substrate are investigated using ultrafast time-resolved optical spectroscopy. The number and characteristics of the detected acoustic modes are found to vary with nanodisk geometry. In particular, their quality factors strongly depend on nanodisk aspect ratio (i.e., diameter over height ratio), reaching a maximal value of ≈70, higher than those previously measured for substrate-supported nano-objects. The peculiarities of the detected acoustic vibrations are confirmed by finite-element simulations, and interpreted as the result of substrate-induced hybridization between the vibrational modes of a nanodisk. The present findings demonstrate novel possibilities for engineering the vibrational modes of nano-objects.

Acoustic Mode Hybridization in a Single Dimer of Gold Nanoparticles.

The acoustic vibrations of single monomers and dimers of gold nanoparticles were investigated by measuring for the first time their ultralow-frequency micro-Raman scattering. This experiment provides access not only to the frequency of the detected vibrational modes but also to their damping rate, which is obscured by inhomogeneous effects in measurements on ensembles of nano-objects. This allows a detailed analysis of the mechanical coupling occurring between two close nanoparticles (mediated by the polymer surrounding them) in the dimer case. Such coupling induces the hybridization of the vibrational modes of each nanoparticle, leading to the appearance in the Raman spectra of two ultralow-frequency modes corresponding to the out-of-phase longitudinal and transverse (with respect to the dimer axis) quasi-translations of the nanoparticles. Additionally, it is also shown to shift the frequency of the quadrupolar modes of the nanoparticles. Experimental results are interpreted using finite-element simulations, which enable the unambiguous identification of the detected modes and despite the simplifications made lead to a reasonable reproduction of their measured frequencies and quality factors. The demonstrated feasibility of low-frequency Raman scattering experiments on single nano-objects opens up new possibilities to improve the understanding of nanoscale vibrations with this technique being complementary with single nano-object time-resolved spectroscopy as it gives access to different vibrational modes.

Mechanical Vibrations of Atomically Defined Metal Clusters: From Nano- to Molecular-Size Oscillators.

Acoustic vibrations of small nanoparticles are still ruled by continuum mechanics laws down to diameters of a few nanometers. The elastic behavior at lower sizes (<1-2 nm), where nanoparticles become molecular clusters made by few tens to few atoms, is still little explored. The question remains to which extent the transition from small continuous-mass solids to discrete-atom molecular clusters affects their specific low-frequency vibrational modes, whose period is classically expected to linearly scale with diameter. Here, we investigate experimentally by ultrafast time-resolved optical spectroscopy the acoustic response of atomically defined ligand-protected metal clusters Au n(SR) m with a number n of atoms ranging from 10 to 102 (0.5-1.5 nm diameter range). Two periods, corresponding to fundamental breathing- and quadrupolar-like acoustic modes, are detected, with the latter scaling linearly with cluster diameters and the former taking a constant value. Theoretical calculations based on density functional theory (DFT) predict in the case of bare clusters vibrational periods scaling with size down to diatomic molecules. For ligand-protected clusters, they show a pronounced effect of the ligand molecules on the breathing-like mode vibrational period at the origin of its constant value. This deviation from classical elasticity predictions results from mechanical mass-loading effects due to the protecting layer. This study shows that clusters characteristic vibrational frequencies are compatible with extrapolation of continuum mechanics model down to few atoms, which is in agreement with DFT computations.

Fano Interference in the Optical Absorption of an Individual Gold-Silver Nanodimer.

Fano resonances are central features in the responses of many systems including atoms, molecules, and nanomaterials. They arise as a consequence of interferences between two channels, most frequently associated with two system modes. In plasmonic materials, Fano interferences between optical modes have been shown, experimentally and theoretically, to induce narrow features in their scattering spectra. By investigating individual silver-gold heterodimers, we first experimentally demonstrate that Fano interference is also a key effect in the optical absorption of plasmonic nano-objects, in agreement with theoretical predictions. Conversely to previously investigated systems, the two interacting modes at the origin of absorptive Fano effect are mostly localized on either one or the other dimer component. Experimental results were obtained by selectively monitoring the optical absorption of one dimer component using a two-color nonlinear time-resolved technique. This also opens the way to full optical far-field noncontact investigations of charge or energy exchanges between nano-objects with a spatial resolution much smaller than the optical wavelength.

Optical absorption and scattering spectroscopies of single nano-objects.

Developments of optical detection and spectroscopy methods for single nano-objects are key advances for applications and fundamental understanding of the novel properties exhibited by nanosize systems. These methods are reviewed, focusing on far-field optical approaches based on light absorption and elastic scattering. The principles of the main linear and nonlinear methods are described and experimental results are illustrated in the case of metal nanoparticles, stressing the key role played by the object environment, such as the presence of a substrate, bound surface molecules or other nano-objects. Special attention is devoted to quantitative methods and correlation of the measured optical spectra of a nano-object with its morphology, characterized either optically or by electron microscopy, as this permits precise comparison with theoretical models. Application of these methods to optical detection and spectroscopy for single semiconductor nanowires and carbon nanotubes is also presented. Extension to ultrafast nonlinear extinction or scattering spectroscopies of single nano-objects is finally discussed in the context of investigation of their nonlinear optical response and their electronic, acoustic and thermal properties.

Size-dependent surface plasmon resonance broadening in nonspherical nanoparticles: single gold nanorods.

The dependence of the spectral width of the longitudinal localized surface plasmon resonance (LSPR) of individual gold nanorods protected by a silica shell is investigated as a function of their size. Experiments were performed using the spatial modulation spectroscopy technique that permits determination of both the spectral characteristics of the LSPR of an individual nanoparticle and its morphology. The measured LSPR is shown to broaden with reduction of both the nanorod length and its diameter, which is in contrast with the predictions of existing classical and quantum theoretical models. This behavior can be reproduced assuming the LSPR width linearly depends on the inverse of an effective length proportional to the square root of the particle surface with the same slope as that recently determined for silica-coated silver nanospheres.

Impact of supporting nanometric membranes on the thermo-optical dynamics of individual plasmonic nanodisks.

The thermal dynamics and transient optical response of individual gold nanodisks supported on thin silicon nitride membranes were investigated using optical time-resolved pump-probe spectroscopy and finite-element modeling. The effect of reducing the membrane thickness from 50 nm to 15 nm on the nanodisk thermal dynamics was explored. A significant deceleration of the nanodisk cooling kinetics was observed, and linked to a quasi-two-dimensional heat diffusion process within the 15 nm thick membrane, without detectable modification of its thermal conductivity. Systematic measurements involving different optical probe wavelengths additionally revealed the contribution of indirect membrane heating to the measured time-resolved signals, an effect particularly pronounced in the spectral range where direct optical heating of the nanodisk induces minimal ultrafast modifications of its extinction cross-section.

Damping of the acoustic vibrations of a suspended gold nanowire in air and water environments.

The lifetimes of the acoustic vibrations of metal nanostructures depend sensitively on the properties of the environment, such as the acoustic impedance and viscosity. In order to accurately study these effects, they have to be separated from the damping processes that are inherent to the nanostructure. Here we show that this can be done experimentally by investigating individual gold nanowires suspended over a trench in air and liquid environments. The experiments were done by ultrafast pump-probe microscopy, recording transient absorption traces at the same point on the nanowire in both environments. These first experiments were performed with water, and the measured vibrational quality factors due to the presence of water were compared to continuum mechanics calculations for a cylinder in a homogeneous environment. Good agreement was found between the experimental quality factors and the calculated values. The continuum mechanics analysis shows that damping is dominated by the acoustic impedance of the solvent rather than by its viscosity for the nanowires in the present experiments. This experimental technique opens up the possibility of studying the effect of viscosity on the high frequency vibrational motions of nanostructures for a variety of liquids.

Cooling Dynamics of Individual Gold Nanodisks Deposited on Thick Substrates and Nanometric Membranes.

The cooling dynamics of individual gold nanodisks synthesized using colloidal chemistry and deposited on solid substrates with different compositions and thicknesses were investigated using optical time-resolved spectroscopy and finite-element modeling. Experiments demonstrate a strong substrate-dependence of these cooling dynamics, which require the combination of heat transfer at the nanodisk/substrate interface and heat diffusion in the substrate. In the case of nanodisks deposited on a thick sapphire substrate, the dynamics are found to be mostly limited by the thermal resistance of the gold/sapphire interface, for which a value similar to that obtained in the context of previous experiments on sapphire-supported single gold nanodisks produced by electron beam lithography is deduced. In contrast, the cooling dynamics of nanodisks supported by nanometric silica and silicon nitride membranes are much slower and largely affected by heat diffusion in the membranes, whose efficiency is strongly reduced as compared to the thick sapphire case.

Surface plasmon resonance properties of single elongated nano-objects: gold nanobipyramids and nanorods.

The spectral characteristics (wavelength and line width) and the optical extinction cross-section of the longitudinal localized surface plasmon resonance (LSPR) of individual gold nanobipyramids have been quantitatively measured using the spatial modulation spectroscopy technique. The morphology of the same individual nanoparticles has been determined by transmission electron microscopy (TEM). The experimental results are thus interpreted with a numerical model using the TEM measured sizes of the particles as an input, and either including the substrate or assuming a mean homogeneous environment. Results are compared to those obtained for individual nanorods and also show the importance of the local environment of the particle on the detailed description of its spectral position and extinction amplitude.

Acoustic vibrations of metal-dielectric core-shell nanoparticles.

The acoustic vibrations of metal nanoparticles encapsulated in a dielectric shell (Ag@SiO(2)) were investigated using a time-resolved femtosecond technique. The measured vibration periods significantly differ from those predicted for the bare metal cores and, depending on the relative core and shell sizes, were found to be either larger or smaller than them. These results show that the vibration of the whole core-shell particle is excited and detected. Moreover, vibrational periods are in excellent agreement with the predictions of a model based on continuum thermoelasticity. However, such agreement is obtained only if a good mechanical contact of the metal and dielectric parts of the core-shell particle is assumed, providing a unique way to probe this contact in multimaterial or hybrid nano-objects.

Ultrafast nano generation of acoustic waves in water via a single carbon nanotube.

Generation of ultra high frequency acoustic waves in water is key to nano resolution sensing, acoustic imaging and theranostics. In this context water immersed carbon nanotubes (CNTs) may act as an ideal optoacoustic source, due to their nanometric radial dimensions, peculiar thermal properties and broad band optical absorption. The generation mechanism of acoustic waves in water, upon excitation of both a single-wall (SW) and a multi-wall (MW) CNT with laser pulses of temporal width ranging from 5 ns down to ps, is theoretically investigated via a multiscale approach. We show that, depending on the combination of CNT size and laser pulse duration, the CNT can act as a thermophone or a mechanophone. As a thermophone, the CNT acts as a nanoheater for the surrounding water, which, upon thermal expansion, launches the pressure wave. As a mechanophone, the CNT acts as a nanopiston, its thermal expansion directly triggering the pressure wave in water. Activation of the mechanophone effect is sought to trigger few nanometers wavelength sound waves in water, matching the CNT acoustic frequencies. This is at variance with respect to the commonly addressed case of water-immersed single metallic nano-objects excited with ns laser pulses, where only the thermophone effect significantly contributes. The present findings might be of impact in fields ranging from nanoscale non-destructive testing to water dynamics at the meso to nanoscale.

Dynamics of phosphodiester synthesis by DNA ligase.

Ligases are essential actors in DNA replication, recombination, and repair by virtue of their ability to seal breaks in the phosphodiester backbone. Ligation proceeds through a nicked DNA-adenylate intermediate (AppDNA), which must be sealed quickly to avoid creating a potentially toxic lesion. Here, we take advantage of ligase-catalyzed AMP-dependent incision of a single supercoiled DNA molecule to observe the step of phosphodiester synthesis in real time. An exponentially distributed number of supercoils was relaxed per successful incision-resealing event, from which we deduce the torque-dependent ligation probability per DNA swivel. Premature dissociation of ligase from nicked DNA-adenylate accounted for approximately 10% of the observed events. The ability of ligase to form a C-shaped protein clamp around DNA is a key determinant of ligation probability per turn and the stability of the ligase-AppDNA intermediate. The estimated rate of phosphodiester synthesis by DNA ligase (400 s(-1)) is similar to the high rates of phosphodiester synthesis by replicative DNA polymerases.

Probing elasticity at the nanoscale: Terahertz acoustic vibration of small metal nanoparticles.

The acoustic response of surface-controlled metal (Pt) nanoparticles is investigated in the small size range, between 1.3 and 3 nm (i.e., 75-950 atoms), using time-resolved spectroscopy. Acoustic vibration of the nanoparticles is demonstrated, with frequencies ranging from 1.1 to 2.6 THz, opening the way to the development of THz acoustic resonators. The frequencies, measured with a noncontact optical method, are in excellent agreement with the prediction of a macroscopic approach based on the continuous elastic model, together with the bulk material elastic constants. This demonstrates the validity of this model at the nanoscale and the weak impact of size reduction on the elastic properties of a material, even for nanoparticles formed by less than 100 atoms.

Versatile template-directed synthesis of gold nanocages with a predefined number of windows.

Highly symmetrical gold nanocages can be produced with a controllable number of circular windows of either 2, 3, 4, 6 or 12 via an original fabrication route. The synthetic pathway includes three main stages: the synthesis of silica/polystyrene multipod templates, the regioselective seeded growth of a gold shell on the unmasked part of the silica surface and the development of gold nanocages by dissolving/etching the templates. Electron microscopy and tomography provide evidence of the symmetrical features of the as-obtained nanostructures. The optical properties of nanocages with 4 and 12 windows were measured at the single particle level by spatial modulation spectroscopy and correlated with numerical simulations based on finite-element modeling. The new multi-step synthesis approach reported here also allows the synthesis of rattle-like nanostructures through filling of the nanocages with a guest nano-object. With the potential to adjust the chemical composition, size and geometry of both the guest particle and the host cage, it opens new routes towards the fabrication of hollow nanostructures of high interest for a variety of applications including sensing devices, catalytic reactors and biomedicine.

Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence.

The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIB-DNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drug-bound TopIB at a single DNA sequence in real time. This is accomplished by covalently linking camptothecins to a triple helix-forming oligonucleotide that binds at one location on the DNA molecule monitored. Surprisingly, we find that the DNA dynamics with the TopIB-drug interaction restricted to a single DNA sequence are indistinguishable from the dynamics observed when the TopIB-drug interaction takes place at multiple sites. Specifically, the DNA sequence does not affect the instantaneous supercoil removal rate or the degree to which camptothecins increase the lifetime of the covalent complex. Our data suggest that sequence-dependent dynamics need not to be taken into account in efforts to develop novel camptothecins.

Multicolor detection of combed DNA molecules using quantum dots.

DNA combing is a useful strategy for manipulating single DNA molecules and has a wide range of applications in genetics, single molecule studies, and nanobiotechnology. Visualization of combed DNA molecules is usually performed by using DNA binding organic dyes. Such dyes are not suitable in all circumstances, especially because of their photoreactivity. We have developed a method for the detection of combed DNA molecules by fluorescence microscopy that avoids the use of DNA-staining agents and does not perturb the structure of the DNA molecule. Biotin- and/or digoxigenin-modified DNA fragments are covalently linked at both ends of a DNA molecule via sequence-specific hybridization and subsequent ligation. After the modified DNA molecules have been combed on a polystyrene-coated surface, their ends are visualized by multicolor fluorescence microscopy using conjugated quantum dots.

Signatures of Small Morphological Anisotropies in the Plasmonic and Vibrational Responses of Individual Nano-objects.

The plasmonic and vibrational properties of single gold nanodisks patterned on a sapphire substrate are investigated via spatial modulation and pump-probe optical spectroscopies. The features of the measured extinction spectra and time-resolved signals are highly sensitive to minute deviations of the nanodisk morphology from a perfectly cylindrical one. An elliptical nanodisk section, as compared to a circular one, lifts the degeneracy of the two nanodisk in-plane dipolar surface plasmon resonances, which can be selectively excited by controlling the polarization of the incident light. This splitting effect, whose amplitude increases with nanodisk ellipticity, correlates with the detection of additional vibrational modes in the context of time-resolved spectroscopy. Analysis of the measurements is performed through the combination of optical and acoustic numerical models. This allows us first to estimate the dimensions of the investigated nanodisks from their plasmonic response and then to compare the measured and computed frequencies of their detectable vibrational modes, which are found to be in excellent agreement. This study demonstrates that single-particle optical spectroscopies are able to provide access to fine morphological characteristics, representing in this case a valuable alternative to traditional techniques aimed at postfabrication inspection of subwavelength nanodevice morphology.

Ultrafast electron-lattice thermalization in copper and other noble metal nanoparticles.

Using time-resolved ultrafast pump-probe spectroscopy we investigated the electron-lattice energy transfer in small copper nanospheres with diameters ranging from 3.2 to 23 nm, either embedded in a glass or dispersed in a solvent. Electron-lattice scattering rate is shown to increase with size reduction, in agreement with our previous results obtained on gold and silver nanoparticles in the low excitation regime. We attribute this effect to the reduction of the screening efficiency of electron-phonon interactions close to the nanoparticle surface. To understand the discrepancy between the results on the electron-lattice scattering in different metals reported in the literature (reduction, no dependence or increase with nanoparticle size), we discuss the experimental conditions required for the accurate determination of electron-lattice energy transfer time from time-resolved investigations in the weak and strong excitation regimes and present power-dependent experiments on gold nanospheres in solution. Our findings are derived from a theoretical analysis based on the two-temperature model predictions and on a complete modeling of the nanoparticle transient extinction cross-section through the resolution of Boltzmann equation in the presence of hot electrons.